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Synthetic DNA and RNA Programming

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ISBN: 9783039217342 / 9783039217359 Year: Pages: 188 DOI: 10.3390/books978-3-03921-735-9 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:16
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Dear Colleagues, Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering and omics technologies. These technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease.

Keywords

fluorescent reporter --- live cell imaging --- microRNA quantification --- optogenetics --- small molecule drug screening --- Escherichia coli --- recombinant protein production --- gene overexpression --- growth effect --- ASKA collection --- codon bias --- branched-chain amino acids --- gene ontology --- genetic code expansion --- protein kinase B --- phosphoinositide dependent kinase 1 --- phosphoseryl-tRNA synthetase --- tRNASep --- alanyl-tRNA synthetase --- class II aminoacyl-tRNA synthetase --- expanded genetic code --- lysine acetylation --- posttranslational modification --- genetic code expansion --- transfer RNA --- synthetic biology --- non-canonical amino acids --- selenocysteine --- genetic code expansion --- release factor 1 --- amber stop codon suppression --- M. jannaschii orthogonal pair --- fluorescence-based screen --- cyclic peptides --- biopharmaceuticals --- mRNA display --- yeast two hybrid --- tRNASer --- mistranslation --- anticodon --- functional conservation --- alternative amino acid and nucleotide repertoires --- alternative core cellular chemistries --- biocontainment --- genetic firewall --- genetic isolation --- orthogonal central dogma of molecular biology --- synthetic life --- xenobiology --- genome engineering --- synthetic biology --- yeasts --- Metschnikowia --- genetic tools --- DNA delivery --- CUG-Ser --- reverse polymerization --- tRNA editing --- tRNA repair --- protein engineering --- synthetic biology --- tRNA --- misacylation --- indirect tRNA aminoacylation --- AspRS --- GluRS-like --- genetic code expansion --- genome synthesis --- genome editing --- microRNA --- protein modification --- RNA metabolism --- tRNA --- synthetic biology --- unnatural amino acids --- unnatural nucleotides

Methods in Computational Biology

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ISBN: 9783039211630 / 9783039211647 Year: Pages: 214 DOI: 10.3390/books978-3-03921-164-7 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Computer Science
Added to DOAB on : 2019-08-28 11:21:27
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Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measurement

Cell-Free Synthetic Biology

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ISBN: 9783039280223 / 9783039280230 Year: Pages: 152 DOI: 10.3390/books978-3-03928-023-0 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: General and Civil Engineering --- Technology (General)
Added to DOAB on : 2020-01-30 16:39:46
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Cell-free synthetic biology is in the spotlight as a powerful and rapid approach to characterize and engineer natural biological systems. The open nature of cell-free platforms brings an unprecedented level of control and freedom for design compared to in vivo systems. This versatile engineering toolkit is used for debugging biological networks, constructing artificial cells, screening protein library, prototyping genetic circuits, developing new drugs, producing metabolites, and synthesizing complex proteins including therapeutic proteins, toxic proteins, and novel proteins containing non-standard (unnatural) amino acids. The book consists of a series of reviews, protocols, benchmarks, and research articles describing the current development and applications of cell-free synthetic biology in diverse areas.

Recent Advances in Biocatalysis and Metabolic Engineering for Biomanufacturing

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ISBN: 9783039215744 / 9783039215751 Year: Pages: 278 DOI: 10.3390/books978-3-03921-575-1 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Technology (General) --- Biotechnology
Added to DOAB on : 2019-12-09 11:49:15
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The use of biocatalysts, including enzymes and metabolically engineered cells, has attracted a great deal of attention in the chemical and bio-industry, because biocatalytic reactions can be conducted under environmentally-benign conditions and in more sustainable ways. The catalytic efficiency and chemo-, regio-, and stereo-selectivity of enzymes can be enhanced and modulated using protein engineering. Metabolic engineering seeks to enhance cellular biosynthetic productivity of target metabolites via controlling and redesigning metabolic pathways using multi-omics analysis, genome-scale modeling, metabolic flux control, and reconstruction of novel pathways. The aim of this book is to cover the recent advances in biocatalysis and metabolic engineering for biomanufacturing of biofuels, chemicals, biomaterials, and pharmaceuticals. Reviews and original research articles on the development of new strategies to improve the catalytic efficiency of enzymes, biosynthetic capability of cell factories, and their applications in production of various bioproducts and chemicals are included.

Keywords

artificial self-sufficient P450 --- bioplastics --- dodecanoic acid --- Nylon 12 --- ?-aminododecanoic acid --- immobilization --- fluorescein diacetate --- polyurethane foam --- biofilm --- total enzymatic activity --- biocatalysis --- Combi-CLEAs --- cascade reactions --- immobilization --- Myceliophthora --- glyoxal oxidase --- 5-hydroxymethylfurfural --- aerobic methane bioconversion --- bioreactor --- string film reactor --- mass transfer performance --- cross-linked enzyme aggregate --- amyloglucosidase --- magnetic nanoparticles --- bovine serum albumin --- polyethyleneimine --- starch hydrolysis --- Eversa --- interfacial activation --- lipase immobilization --- enzyme stabilization --- enzyme modulation --- metabolic engineering --- synthetic biology --- 3-hydroxypropionic acid --- microbial production --- fatty acid synthesis --- acetate --- redox enzymes --- FTIR spectroscopy --- small molecules --- Corynebacterium glutamicum --- Pvgb --- tunable expression system --- expression vectors --- synthetic biology --- Vitreoscilla --- vgb --- biocatalysts --- biocatalytic reaction --- Methylosinus sporium strain 5 --- soluble methane monooxygenase --- C–H activation --- O2 activation --- synthetic biology --- metabolic engineering --- microbial cell factory --- synthetic metabolic pathways --- mannose --- magnetic nanoparticles --- immobilization --- whole cell --- specific recognition --- 12-hydroxydodecanoic acid --- dodecanoic acid --- CYP153A --- whole-cell biotransformation --- Candida antarctica Lipase B --- transesterification --- polymer functionalization --- tetraethylene glycol --- poly(ethylene glycol) --- hydrogenase --- bio-hydrogen --- chemicals addition --- review --- (?)-?-bisabolol --- mevalonate (MVA) --- mevalonate kinase 1 --- Methanosarcina mazei --- fed-batch fermentation --- monoterpene --- prokaryotic microbial factory --- metabolic engineering --- MEP pathway --- MEV pathway --- n/a

Dynamics Days Latin America and the Caribbean 2018

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ISBN: 9783039215034 / 9783039215041 Year: Pages: 142 DOI: 10.3390/books978-3-03921-504-1 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Mathematics
Added to DOAB on : 2019-12-09 16:10:12
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This book contains various works presented at the Dynamics Days Latin America and the Caribbean (DDays LAC) 2018. Since its beginnings, a key goal of the DDays LAC has been to promote cross-fertilization of ideas from different areas within nonlinear dynamics. On this occasion, the contributions range from experimental to theoretical research, including (but not limited to) chaos, control theory, synchronization, statistical physics, stochastic processes, complex systems and networks, nonlinear time-series analysis, computational methods, fluid dynamics, nonlinear waves, pattern formation, population dynamics, ecological modeling, neural dynamics, and systems biology. The interested reader will find this book to be a useful reference in identifying ground-breaking problems in Physics, Mathematics, Engineering, and Interdisciplinary Sciences, with innovative models and methods that provide insightful solutions. This book is a must-read for anyone looking for new developments of Applied Mathematics and Physics in connection with complex systems, synchronization, neural dynamics, fluid dynamics, ecological networks, and epidemics.

Disease and the Hippo Pathway: Cellular and Molecular Mechanisms

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ISBN: 9783039217762 / 9783039217779 Year: Pages: 226 DOI: 10.3390/books978-3-03921-777-9 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:16
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The Hippo pathway is a highly dynamic cellular signaling nexus that plays central roles in multiple cell types and regulates regeneration, metabolism, and development. The Hippo pathway integrates mechanotransduction, cell polarity, inflammation, and numerous types of paracrine signaling. If not tightly regulated, dysregulated Hippo pathway signaling drives the onset and progression of a range of diseases, including fibrosis and cancer. The molecular understanding of the Hippo pathway is rapidly evolving. This Special Issue contains ten articles contributed by established and up-and-coming Hippo pathway experts that, as a whole, provides an up-to-date overview of how dysregulated Hippo pathway activity is a common driver of specific diseases. The articles have a particular focus on the underlying molecular and cellular mechanisms that cause the Hippo pathway to go awry, and especially how this drives disease. The articles analyze disease-specific as well as common themes, which provides valuable insights into the fundamental molecular mechanisms in the dysfunctioning Hippo pathway, and thereby offer practical insights into potential future therapeutic intervention strategies.

Contemporary Natural Philosophy and Philosophies - Part 1

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ISBN: 9783038978220 / 9783038978237 Year: Pages: 350 DOI: 10.3390/books978-3-03897-823-7 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Philosophy
Added to DOAB on : 2019-06-26 08:44:06
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Modern information communication technology eradicates barriers of geographic distances, making the world globally interdependent, but this spatial globalization has not eliminated cultural fragmentation. The Two Cultures of C.P. Snow (that of science–technology and that of humanities) are drifting apart even faster than before, and they themselves crumble into increasingly specialized domains. Disintegrated knowledge has become subservient to the competition in technological and economic race leading in the direction chosen not by the reason, intellect, and shared value-based judgement, but rather by the whims of autocratic leaders or fashion controlled by marketers for the purposes of political or economic dominance. If we want to restore the authority of our best available knowledge and democratic values in guiding humanity, first we have to reintegrate scattered domains of human knowledge and values and offer an evolving and diverse vision of common reality unified by sound methodology. This collection of articles responds to the call from the journal Philosophies to build a new, networked world of knowledge with domain specialists from different disciplines interacting and connecting with other knowledge-and-values-producing and knowledge-and-values-consuming communities in an inclusive, extended, contemporary natural–philosophic manner. In this process of synthesis, scientific and philosophical investigations enrich each other—with sciences informing philosophies about the best current knowledge of the world, both natural and human-made—while philosophies scrutinize the ontological, epistemological, and methodological foundations of sciences, providing scientists with questions and conceptual analyses. This is all directed at extending and deepening our existing comprehension of the world, including ourselves, both as humans and as societies, and humankind.

Keywords

n/a --- compositional hierarchy --- development --- dissipative structures --- final cause --- internalism --- Second Law of thermodynamics --- subsumptive hierarchy --- agonism --- apophasis --- autocatalysis --- centripetality --- contingency --- endogenous selection --- heterogeneity --- indeterminacy --- process --- mathematics --- physics --- philosophical foundations --- natural philosophy --- the logic of nature --- ontology --- epistemology --- in the name of nature --- philosophy of information --- natural philosophy --- metaphysics --- physics --- problem of induction --- physicalism --- theoretical unity --- philosophy of science --- scientific method --- scientific progress --- pessimistic induction --- awareness --- cognition --- computation --- cybernetics --- differentiation --- fitness --- holographic encoding --- memory --- perception --- quantum information --- signal transduction --- spatial representation --- thermodynamics --- unitarity --- Leibniz --- monad --- internal quantum state --- relational biology --- reflexive psychology --- self --- induction --- naturalism --- evidence and justification --- epistemic norms --- induction and concept formation --- induction and discovery of laws --- natural philosophy --- R.M. Unger --- L. Smolin --- Aristotle --- F.W.J. Schelling --- Naturphilosophie --- A.N. Whitehead --- Ivor Leclerc --- dialectics --- discourse --- discursive space --- information --- knowledge --- humanistic management --- language --- natural philosophy --- subjective experience --- process --- dual aspects --- consciousness --- information-theory --- theoretical biology --- 1st-person and 3rd-person perspectives --- hylomorphism --- mind --- form --- matter --- neurodynamics --- natural philosophy --- philosophy of science --- Jungian psychology --- depth psychology --- analytical psychology --- phenomenological psychology --- evolutionary psychology --- active imagination --- Aristotle’s four causes --- aesthetics in science --- philosophy as a way of life --- common good --- contradiction --- ethics --- information --- logic --- naturalization --- realism --- science --- synthesis --- natural philosophy --- philosophy of nature --- naturalism --- unity of knowledge --- qualitative ontology --- intentionality --- dispositions --- qualia --- abduction --- agent-based reasoning --- creativity --- eco-cognitive model --- eco-cognitive openness --- fallacies --- errors of reasoning --- third-way reasoning --- naturalization of logic --- causality --- embodiment --- measurement --- regulation --- retrocausality --- second-person description --- symmetry breaking --- temporality --- natural philosophy --- cosmology --- emptiness --- vacuum --- void --- dark energy --- space flight --- exoplanet --- big freeze --- big crunch --- everyday lifeworld --- digitization --- computability --- complexity --- reverse mathematics --- quantum computing --- real computing --- theory of everything --- acategoriality --- state-space approach --- mental representation --- dual-aspect monism --- exceptional experiences --- intentionality --- mind-matter relations --- category theory --- memory evolutive system --- emergence --- emergentist reductionism --- anticipation --- creativity --- info-computational model

Molecular Mechanism of Alzheimer's Disease

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ISBN: 9783039214075 / 9783039214082 Year: Pages: 228 DOI: 10.3390/books978-3-03921-408-2 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:16
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Alzheimer’s disease (AD) is an age-related neurological disease that affects tens of millions of people, in addition to their carers. Hallmark features of AD include plaques composed of amyloid beta, as well as neurofibrillary tangles of tau protein. However, despite more than a century of study, the cause of Alzheimer’s disease remains unresolved. The roles of amyloid beta and tau are being questioned and other causes of AD are now under consideration. The contributions of researchers, model organisms, and various hypotheses will be examined in this Special Issue.

Keywords

?-secretase --- amyloid beta --- calcium signaling --- drug target discovery --- endoplasmic reticulum --- inositol 1,4,5-trisphosphate receptor --- ion channel --- oxidative stress --- ryanodine receptor --- therapy --- amyloid-? oligomer --- protein aggregation --- A?O receptors --- Alzheimer’s disease --- neurodegeneration --- amyloid ? --- Alzheimer’s disease --- cognitive function --- dairy products --- dementia --- inflammation --- microglia --- Alzheimer’s disease --- yeast --- Tau --- amyloid ? --- ubiquitin --- aggregation --- oligomerization --- prion --- CDK5R1 --- lncRNAs --- Alzheimer’s disease --- miR-15/107 --- NEAT1 --- HOTAIR --- MALAT1 --- heat shock response --- heat shock protein --- Alzheimer’s disease --- beta amyloid --- yeast --- Alzheimer’s disease --- complement receptor 1 --- CR1 length polymorphism --- CR1 density --- complement C3b/C4b receptor --- complement --- dementia --- molecular biology --- neurosciences --- genetic risk --- Alzheimer’s disease --- brain glucose metabolism --- neuronal differentiation --- neuronal degeneration --- Prolyl isomerases --- Pin1 --- type 2 diabetes --- type 3 diabetes --- miR-34c --- dendritic spine --- Alzheimer’s disease --- Alzheimer’s disease --- positron emission tomography (PET) --- magnetic resonance imaging (MRI) --- Alzheimer’s disease --- cystathionine-?-lyase CTH gene --- DNA methylation --- epigenetics --- epigenome-wide association study --- methylome --- methylenetetrahydrofolate reductase MTHFR gene --- nutrition --- S-adenosylmethionine --- vitamin B complex --- Alzheimer’s disease --- sleep disturbance --- sleep fragmentation --- slow-wave sleep --- amyloid beta --- tau --- proteostasis --- default-mode network --- cognitive behavioral therapy for insomnia --- APOE gene --- apolipoprotein E --- DNA methylation --- mild cognitive impairment --- Hispanics

The Future of Hyperspectral Imaging

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ISBN: 9783039218226 / 9783039218233 Year: Pages: 220 DOI: 10.3390/books978-3-03921-823-3 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2019-12-09 16:39:37
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Keywords

hyperspectral imaging --- Raman --- fluorescence --- sorting --- quality control --- black polymers --- PZT --- classification --- machine learning --- alternating direction method of multipliers --- Cramer–Rao lower bound --- forward observation model --- linear mixture model --- maximum likelihood --- multiband image fusion --- total variation --- fingerprints --- blood detection --- age determination --- hyperspectral imaging --- lossless compression --- multitemporal hyperspectral images --- information theoretic analysis --- predictive coding --- hyperspectral imaging --- plant phenotyping --- disease detection --- spectral tracking --- time series --- hyperspectral imaging --- principal component analysis --- oxygen saturation --- wound healing --- diabetic foot ulcer --- Raman spectroscopy --- chemical imaging --- compressive detection --- spatial light modulators (SLM) --- digital micromirror device (DMD) --- digital light processor (DLP) --- optimal binary filters --- Chemometrics --- multivariate data analysis --- compressive sensing --- hyperspectral imaging --- multiplexing system --- liquid crystal --- three-dimensional imaging --- integral imaging --- remote sensing --- point target detection --- CS-MUSI --- hyperspectral --- video --- imaging --- coastal dynamics --- moving vehicle imaging --- bi-directional reflectance distribution function (BRDF) --- hemispherical conical reflectance factor (HCRF) --- stereo imaging --- digital elevation model --- Virginia Coast Reserve Long Term Ecological Research (VCR LTER) --- Hyperspectral imaging --- painting samples --- retouching pigments --- watercolours --- multivariate analysis --- potatoes --- sprouting --- primordial leaf count --- hyperspectral imaging --- spectroscopy --- fusion --- wavelength selection --- PLSR --- interval partial least squares --- deep learning --- hyperspectral imaging --- neural networks --- machine learning --- image processing --- hyperspectral imaging --- medical imaging by HSI --- HSI for biology --- remote sensing --- hyperspectral microscopy --- fluorescence hyperspectral imaging --- Raman hyperspectral imaging --- infrared hyperspectral imaging --- statistical methods for HSI --- hyperspectral data mining and compression --- statistical methods for HSI --- hyperspectral data mining and compression

Surface Modification to Improve Properties of Materials

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ISBN: 9783038977964 9783038977971 Year: Pages: 356 DOI: 10.3390/books978-3-03897-797-1 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Technology (General) --- General and Civil Engineering
Added to DOAB on : 2019-04-25 16:37:17
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This book contains selected contributions on surface modification to improve the properties of solid materials. The surface properties are tailored either by functionalization, etching, or deposition of a thin coating. Functionalization is achieved by a brief treatment with non-equilibrium gaseous plasma containing suitable radicals that interact chemically with the material surface and thus enable the formation of rather stable functional groups. Etching is performed in order to modify the surface morphology. The etching parameters are selected in such a way that a rich morphology of the surfaces is achieved spontaneously on the sub-micrometer scale, without using masks. The combination of adequate surface morphology and functionalization of materials leads to superior surface properties which are particularly beneficial for the desired response upon incubation with biological matter. Alternatively, the materials are coated with a suitable thin film that is useful in various applications from food to aerospace industries.

Keywords

sulphur hexafluoride (SF6) plasma --- tetrafluoromethane (CF4) plasma --- polymer polyethylene terephthalate (PET) --- surface modification --- functionalization and wettability --- optical emission spectroscopy (OES) --- electronegativity --- PVD nanocomposite coatings --- aluminum die casting --- tool life --- tribological performance --- plasma surface modification --- polymer polypropylene --- neutral oxygen atom density --- initial surface functionalization --- food packaging --- wettability --- tantalum --- hardness --- gradient nanostructured layer --- grain size --- residual stress --- dry wear behavior --- surface texture --- surface treatment --- Ti6Al4V alloy --- tribology --- biology --- materials characterization --- shot-peening --- image processing --- TIG welding --- aluminum 6061-T6 --- special surfaces --- wettability --- superhydrophobic --- cell cultures --- anti-bio adhesion --- self-cleaning fabrics --- polyethylene granules --- low-pressure MW air plasma --- optical emission spectroscopy --- XPS --- laser cobalt catalytic probe --- Alloy 718 --- surface hardness --- surface residual stress --- grain size --- fretting failure --- corrosion --- antimicrobial film --- nisin --- physical properties --- plasma treatment polyvinyl alcohol --- surface characterization --- microhole-textured tool --- CaF2 --- micro-EDM --- tribological properties --- egg shell --- stearic acid --- modification --- particle characterization --- epoxy composites --- dynamic mechanical analysis --- adhesion effectiveness --- Poly(tetrafluoroethylene) --- Teflon --- plasma treatment --- zeta potential --- surface energy --- contact angle measurement --- lectin --- bovine serum albumin --- adsorption --- cellulose thin film --- polystyrene --- gold --- surface plasmon resonance spectroscopy --- silver nanoparticles --- laser ablation in liquids --- laser synthesis of colloidal nanoparticles solution --- nanoparticle-impregnated paper --- antimicrobial activity --- fiber fines --- sheet forming --- vacuum filtration --- pulse power --- electrical stimulation --- electric field --- mushroom --- L. edodes --- Lyophyllum deeastes Sing --- surface modification --- porous silicon --- silicon surface --- carbonization --- oxidation --- aluminum --- alloy --- duralumin --- etching --- surface texture --- porous-like --- adhesive bonding --- superhydrophobic --- porous silicon --- visible light assisted organosilanization --- solid state NMR --- XPS --- ToF-SIMS --- atmospheric pressure plasma jets --- plasma polymerization --- superhydrophobicity --- wetting --- biomaterial --- polymer --- plasma --- functionalization --- surface properties --- thrombosis --- hemocompatibility --- endothealization --- vascular graft --- biocompatibility --- endothelial cells --- surface properties --- nanostructuring --- functionalization --- grafting

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